- The emergent technology of using nanopores for stochastic sensing of biomolecules introduces a demand for the development of simple fabrication methodologies of nanopores in solid state membranes. This process becomes particularly challenging when membranes of composite layer architecture are involved. To overcome this challenge we have employed a focused electron beam induced chemical etching process. We present here the fabrication of nanopores in silicon-on-insulator based membranes in a single step process. In this process, chemical etching of the membrane materials by XeF2 gas is locally accelerated by an electron beam, resulting in local etching, with a top membrane oxide layer preventing delocalized etching of the silicon underneath. Nanopores with a funnel or conical, 3-dimensional (3D) shape can be fabricated, depending on the duration of exposure to XeF2, and their diameter is dominated by the time of exposure to the electron beam. The demonstrated ability to form high-aspect ratio nanopores in comparably thick, multi-layered silicon based membranes allows for an easy integration into current silicon process technology and hence is attractive for implementation in biosensing lab-on-chip fabrication technologies.